R Under development (unstable) (2024-09-06 r87103 ucrt) -- "Unsuffered Consequences"
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> # Test inspired by the harmonic mean example in R-help
> # thread '[R] Beyond double-precision?' on May 9, 2009.
> 
> library("matrixStats")
> library("stats")
> 
> logSumExp0 <- function(lx) {
+   idx_max <- which.max(lx)
+   log1p(sum(exp(lx[-idx_max] - lx[idx_max]))) + lx[idx_max]
+ }
> 
> n <- 200L
> set.seed(1)
> 
> for (mode in c("integer", "double")) {
+   cat("mode: ", mode, "\n", sep = "")
+   x <- matrix(runif(n, min = 1.0, max = 3.0), nrow = 20L)
+   storage.mode(x) <- mode
+   str(x)
+ 
+   # The logarithm of the harmonic mean by rows
+   y_h <- log(1 / rowMeans(1 / x))
+   str(y_h)
+ 
+   lx_neg <- -log(x)
+ 
+   y0 <- log(ncol(x)) - apply(lx_neg, MARGIN = 1L, FUN = logSumExp0)
+   stopifnot(all.equal(y0, y_h))
+ 
+   y1 <- log(ncol(x)) - apply(lx_neg, MARGIN = 1L, FUN = logSumExp)
+   stopifnot(all.equal(y1, y0))
+ 
+   y2 <- log(ncol(x)) - rowLogSumExps(lx_neg)
+   stopifnot(all.equal(y2, y0))
+ 
+   y3 <- log(ncol(x)) - colLogSumExps(t(lx_neg))
+   stopifnot(all.equal(y3, y0))
+ 
+ 
+   # The logarithm of the harmonic mean by columns
+   y_h <- log(1 / colMeans(1 / x))
+   str(y_h)
+ 
+   y0 <- log(nrow(x)) - apply(lx_neg, MARGIN = 2L, FUN = logSumExp0)
+   stopifnot(all.equal(y0, y_h))
+ 
+   y1 <- log(nrow(x)) - apply(lx_neg, MARGIN = 2L, FUN = logSumExp)
+   stopifnot(all.equal(y1, y0))
+ 
+   y2 <- log(nrow(x)) - colLogSumExps(lx_neg)
+   stopifnot(all.equal(y2, y0))
+ 
+   y3 <- log(nrow(x)) - rowLogSumExps(t(lx_neg))
+   stopifnot(all.equal(y3, y0))
+ 
+   # Testing names
+   rownames(lx_neg) <- seq_len(nrow(x))
+   colnames(lx_neg) <- seq_len(ncol(x))
+   y2 <- rowLogSumExps(lx_neg, useNames = TRUE)
+   stopifnot(identical(names(y2), rownames(lx_neg)))
+   y3 <- colLogSumExps(t(lx_neg), useNames = TRUE)
+   stopifnot(identical(names(y3), rownames(lx_neg)))
+ } # for (mode ...)
mode: integer
 int [1:20, 1:10] 1 1 2 2 1 2 2 2 2 1 ...
 num [1:20] 0.357 0.223 0.223 0.288 0.511 ...
 num [1:10] 0.322 0.223 0.322 0.255 0.255 ...
mode: double
 num [1:20, 1:10] 1.54 1.44 2.03 1.54 1.36 ...
 num [1:20] 0.526 0.466 0.734 0.638 0.604 ...
 num [1:10] 0.627 0.582 0.617 0.474 0.418 ...
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Corner cases
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> ## Zero-size matrices
> lx <- matrix(numeric(0L), nrow = 0L, ncol = 0L)
> y <- rowLogSumExps(lx)
> print(y)
numeric(0)
> stopifnot(length(y) == nrow(lx))
> 
> y <- colLogSumExps(lx)
> print(y)
numeric(0)
> stopifnot(length(y) == ncol(lx))
> 
> ## Zero-height matrices
> lx <- matrix(numeric(0L), nrow = 0L, ncol = 5L)
> y <- rowLogSumExps(lx)
> print(y)
numeric(0)
> stopifnot(length(y) == nrow(lx))
> 
> y <- colLogSumExps(lx)
> print(y)
[1] -Inf -Inf -Inf -Inf -Inf
> stopifnot(length(y) == ncol(lx))
> stopifnot(all(y == -Inf))
> 
> ## Zero-width matrices
> lx <- matrix(numeric(0L), nrow = 5L, ncol = 0L)
> y <- colLogSumExps(lx)
> print(y)
numeric(0)
> stopifnot(length(y) == ncol(lx))
> 
> y <- rowLogSumExps(lx)
> print(y)
[1] -Inf -Inf -Inf -Inf -Inf
> stopifnot(length(y) == nrow(lx))
> stopifnot(all(y == -Inf))
> 
> 
> ## Matrices with one element
> lx <- matrix(1.0, nrow = 1L, ncol = 1L)
> y <- rowLogSumExps(lx)
> print(y)
[1] 1
> stopifnot(length(y) == nrow(lx))
> stopifnot(all(y == lx))
> 
> y <- colLogSumExps(lx)
> print(y)
[1] 1
> stopifnot(length(y) == ncol(lx))
> stopifnot(all(y == lx))
> 
> ## All missing values
> lx <- matrix(NA_real_, nrow = 1L, ncol = 1L)
> y <- rowLogSumExps(lx, na.rm = TRUE)
> print(y)
[1] -Inf
> stopifnot(length(y) == nrow(lx))
> stopifnot(identical(y, -Inf))
> 
> lx <- matrix(NA_real_, nrow = 1L, ncol = 1L)
> y <- colLogSumExps(lx, na.rm = TRUE)
> print(y)
[1] -Inf
> stopifnot(length(y) == ncol(lx))
> stopifnot(identical(y, -Inf))
> 
> lx <- matrix(NA_real_, nrow = 2L, ncol = 2L)
> y <- rowLogSumExps(lx, na.rm = TRUE)
> print(y)
[1] -Inf -Inf
> stopifnot(length(y) == nrow(lx))
> stopifnot(all(y == -Inf))
> 
> y <- rowLogSumExps(lx, na.rm = FALSE)
> print(y)
[1] NA NA
> stopifnot(length(y) == nrow(lx))
> stopifnot(all(is.na(y) & !is.nan(y)))
> 
> lx <- matrix(NA_real_, nrow = 2L, ncol = 2L)
> y <- colLogSumExps(lx, na.rm = TRUE)
> print(y)
[1] -Inf -Inf
> stopifnot(length(y) == ncol(lx))
> stopifnot(all(y == -Inf))
> 
> y <- colLogSumExps(lx, na.rm = FALSE)
> print(y)
[1] NA NA
> stopifnot(length(y) == ncol(lx))
> stopifnot(all(is.na(y) & !is.nan(y)))
> 
> ## +Inf values
> lx <- matrix(c(1, 2, +Inf), nrow = 3L, ncol = 2L)
> y <- colLogSumExps(lx, na.rm = TRUE)
> print(y)
[1] Inf Inf
> stopifnot(length(y) == ncol(lx))
> stopifnot(all(y == +Inf))
> 
> ## multiple -Inf values
> lx <- matrix(c(-Inf, -Inf), nrow = 2L, ncol = 3L)
> y <- rowLogSumExps(lx)
> print(y)
[1] -Inf -Inf
> stopifnot(length(y) == nrow(lx))
> stopifnot(all(y == -Inf))
> 
> lx <- matrix(c(-Inf, 5, -Inf), nrow = 2L, ncol = 3L, byrow = TRUE)
> y <- rowLogSumExps(lx)
> print(y)
[1] 5 5
> stopifnot(length(y) == nrow(lx))
> stopifnot(all(y == 5))
> 
> ## Bug report #104 (https://github.com/HenrikBengtsson/matrixStats/issues/104)
> ## (This would core dump on Windows)
> x <- matrix(0.0, nrow = 2L, ncol = 32762L)
> y <- colLogSumExps(x)
> str(y)
 num [1:32762] 0.693 0.693 0.693 0.693 0.693 ...
> 
> ## Bug report #120 (https://github.com/HenrikBengtsson/matrixStats/issues/120)
> ## (This would error if x had rownames/colnames and non-NULL rows/cols were
> ## used)
> x <- matrix(runif(6), nrow = 2L, ncol = 3L,
+             dimnames = list(c("A", "B"), c("a", "b", "c")))
> y <- colLogSumExps(x, cols = 3:1, useNames = TRUE)
> stopifnot(names(y) == c("c", "b", "a"))
> y <- rowLogSumExps(x, rows = 2, useNames = TRUE)
> stopifnot(names(y) == "B")
> 
> 
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> # Check names attributes
> # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
> 
> ## Create isFALSE() if running on an old version of R
> if (!exists("isFALSE", mode="function")) {
+   isFALSE <- function(x) is.logical(x) && length(x) == 1L && !is.na(x) && !x
+ }
> 
> rowLogSumExps_R <- function(x, ..., useNames = NA) {
+   res <- apply(x, MARGIN = 1L, FUN = function(rx, ...) {
+     log(sum(exp(rx), ...))
+   }, ...)
+   if (isFALSE(useNames)) names(res) <- NULL
+   res
+ }
> 
> x <- matrix(runif(6 * 6, min = -6, max = 6), nrow = 6L, ncol = 6L)
> 
> # To check names attribute
> dimnames <- list(letters[1:6], LETTERS[1:6])
> 
> # Test with and without dimnames on x
> for (setDimnames in c(TRUE, FALSE)) {
+   if (setDimnames) dimnames(x) <- dimnames
+   else dimnames(x) <- NULL
+   for (useNames in c(if (!matrixStats:::isUseNamesNADefunct()) NA, TRUE, FALSE)) {
+     y0 <- rowLogSumExps_R(x, useNames = useNames)
+     y1 <- rowLogSumExps(x, useNames = useNames)
+     y2 <- colLogSumExps(t(x), useNames = useNames)
+     stopifnot(all.equal(y1, y0))
+     stopifnot(all.equal(y2, y0))
+   }
+ }
> 
> proc.time()
   user  system elapsed 
   0.32    0.06    0.34